I’m a bit confused with your wording: “who actually killed the traitor numbers”.. but if you mean: “the traitor who actually killed the numbers” then… it’s 003.
My guess based on the story so far:
003 indeed let Ijin go after Ijin said he didn’t killed anyone. But it’s not because loyalty or such, she simply got to realize that this is the chance for her to also run from the camp..
Not to mention, 003 was cold-blooded for real. Like farrr colder than 002 (that’s why they dated I guess?). So killing the injured member was a no brainer for her, killing them was easy. After seeing the body scattered, the camp will automatically think 003 was also dead somewhere in the jungle. She is sure her body won’t be confirmed or retrieved because out of everyone there, only 001 who care enough to bury the comrade’s body properly.

i know this arc is just getting started but im really curious if 003 will somehow be involved be involved bc we havent seen her in a while
im also curious though after rereading --- who actually killed the "traitor" numbers? when ijin was defecting, 003 was fully planning on at least incapacitating ijin until he told her that he didn't kill any of the numbers,, so she let him go... still hate her tho!